Abstract

Background

DNA methylation is an important biochemical mark that silences repetitive sequences,
such as transposons, and reinforces epigenetic gene expression states. An important
class of repetitive genes under epigenetic control in eukaryotic genomes encodes ribosomal
RNA (rRNA) transcripts. The ribosomal genes coding for the 45S rRNA precursor of the
three largest eukaryotic ribosomal RNAs (18S, 5.8S, and 25–28S) are found in nucleolus
organizer regions (NORs), comprised of hundreds to thousands of repeats, only some
of which are expressed in any given cell. An epigenetic switch, mediated by DNA methylation
and histone modification, turns rRNA genes on and off. However, little is known about
the mechanisms that specify and maintain the patterns of NOR DNA methylation.

Results

Here, we explored the extent of naturally-occurring variation in NOR DNA methylation
among accessions of the flowering plant Arabidopsis thaliana. DNA methylation in coding regions of rRNA genes was positively correlated with copy
number of 45S rRNA gene and DNA methylation in the intergenic spacer regions. We investigated
the inheritance of NOR DNA methylation patterns in natural accessions with hypomethylated
NORs in inter-strain crosses and defined three different categories of inheritance
in F1 hybrids. In addition, subsequent analysis of F2 segregation for NOR DNA methylation
patterns uncovered different patterns of inheritance. We also revealed that NOR DNA
methylation in the Arabidopsis accession Bor-4 is influenced by the vim1-1 (variant in methylation 1-1) mutation, but the primary effect is specified by the NORs themselves.

Conclusion

Our results indicate that the NORs themselves are the most significant determinants
of natural variation in NOR DNA methylation. However, the inheritance of NOR DNA methylation
suggests the operation of a diverse set of mechanisms, including inheritance of parental
methylation patterns, reconfiguration of parental NOR DNA methylation, and the involvement
of trans-acting modifiers.